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The 32-year-old opener aggravated his lower back while throwing a ball during the fielding practice at the Basin Reserve on Saturday.
Guptill looked in pain as he walked off the ground with the help of New Zealand physiotherapist Vijay Vallabh and security manager Terry Minish.
Colin Munro, who was left out of the fourth ODI after his scores of 8, 31 and 7 in the first three ODIs, is set to return to the squad.
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“He’s been assessed by team physio Vijay Vallabh & will be reassessed tomorrow morning. Colin Munro will rejoin the ODI squad tomorrow morning.”
India have already secured the five-ODI series after winning the first three games. New Zealand won the fourth match by eight wickets to claw one back.
The injury was not deemed serious and Guptill may be fit to play the first Twenty20 international in Wellington on Wednesday.